Posts by edikedikedikedik

... > I am not sure if they would be considerate enough to re-run the sample at no cost. It would depend on your relationship with them. You could always ask for a discount on a re-run.
Although it would be an ideal outcome, I'm not sure either, since communication is handled by another department. ...

... > Was this the only sample in that lane?
> Do you know what the cluster density for this run was?
> How much phiX was spiked in to this run?
I've updated the question providing answers to these questions. Please, take a look. ...

... Yes, we are running trimmomatic in PE mode (i.e. we trim both files simultaneously). We've reported all surviving reads (not just surviving pairs). The genome is presumably 170kbp long, and we expect ~50-70x coverage (given surviving pairs). It is enough for assembly, though it might not be sufficie ...

... Thank you for a response.
> Was this the only sample in that lane? How much
> phiX was spiked in to this run?
As far as we can tell there were 4 samples with largely different phage genomes. And they all exhibit these quality issues. We'll clarify if there might've been any other sample pr ...

... Having received a task to assemble phage genome, I and my colleague ran into several problems.
- First, the sequence duplication levels are abnormally high, reaching up to ~90% and ~40% for forward and reverse reads, respectively.
![Sequence duplication level for raw forward R1 reads][1]
- Secon ...